Covers: Chapter 15 - Unit tests

Unit Testing

Framework choice

• Bioconductor slightly prefers testthat. RUnit and tinytest are also accepted.
• testthat: active development, rich assertions, integrates with devtools, informative failures.
• tinytest: lightweight, zero dependencies.
• RUnit: long Bioconductor history but unmaintained since ~2010.
• Declare the framework in DESCRIPTION Suggests: (e.g. Suggests: testthat, or Suggests: RUnit, BiocGenerics, or Suggests: tinytest).

Directory structure and naming

• testthat: tests in tests/testthat/, files start with test. Set up with usethis::use_testthat().
• RUnit: tests in inst/unitTests/, files match test_*.R (e.g. test_divideBy.R). Add tests/runTests.R containing: BiocGenerics:::testPackage("MyPackage").
• tinytest: tests in inst/tinytest/. Add tests/tinytest.R: if (requireNamespace("tinytest", quietly=TRUE)) tinytest::test_package("PACKAGE").

What to test

• Test functions, methods, and classes with known inputs and expected outputs.
• Test edge cases and error conditions, not only the happy path.
• No hard minimum coverage percentage is mandated, but higher coverage is expected and reduces bug risk.

Coverage measurement

• Use the covr package: covr::package_coverage().

Running tests

• Full check (runs all tests): R CMD check MyPackage.
• During development: devtools::test() (reloads code and reruns).
• Manual: source the package and test files, then call the test function.

Long-running tests

• Consult the bioc-devel mailing list before adding tests that run very long, so they do not slow the nightly builds.

Source: Unit tests Fetched 2026-08-14 from contributions.bioconductor.org (Bioconductor devel guide).